Last updated on 2025-03-12 08:52:57 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-gcc | 1.0.2 | 9.06 | 84.03 | 93.09 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.0.2 | 240.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.2 | 287.36 | OK | |||
| r-devel-macos-arm64 | 1.0.2 | 116.00 | OK | |||
| r-devel-macos-x86_64 | 1.0.2 | 178.00 | OK | |||
| r-devel-windows-x86_64 | 1.0.2 | 16.00 | 181.00 | 197.00 | OK | |
| r-patched-linux-x86_64 | 1.0.2 | OK | ||||
| r-release-macos-arm64 | 1.0.2 | 100.00 | OK | |||
| r-release-macos-x86_64 | 1.0.2 | 138.00 | OK | |||
| r-release-windows-x86_64 | 1.0.2 | 20.00 | 192.00 | 212.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.2 | 68.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 1.0.2 | 138.00 | OK |
Version: 1.0.2
Check: examples
Result: ERROR
Running examples in ‘jamba-Ex.R’ failed
The error most likely occurred in:
> ### Name: kable_coloring
> ### Title: Extend kableExtra colorization of 'Rmarkdown' tables
> ### Aliases: kable_coloring
>
> ### ** Examples
>
> ## Don't show:
> if (all(check_pkg_installed(c("circlize", "kableExtra")))) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf
+ ## End(Don't show)
+ expt_df <- data.frame(
+ Sample_ID="",
+ Treatment=rep(c("Vehicle", "Dex"), each=6),
+ Genotype=rep(c("Wildtype", "Knockout"), each=3),
+ Rep=paste0("rep", c(1:3)))
+ expt_df$Sample_ID <- pasteByRow(expt_df[, 2:4])
+
+ # define colors
+ colorSub <- c(Vehicle="palegoldenrod",
+ Dex="navy",
+ Wildtype="gold",
+ Knockout="firebrick",
+ nameVector(
+ color2gradient("grey48", n=3, dex=10),
+ rep("rep", 3),
+ suffix=""),
+ nameVector(
+ color2gradient(n=3,
+ c("goldenrod1", "indianred3", "royalblue3", "darkorchid4")),
+ expt_df$Sample_ID))
+ kbl <- kable_coloring(
+ expt_df,
+ caption="Experiment design table showing categorical color assignment.",
+ colorSub)
+ # Note that the HTML table is rendered in 'Rmarkdown', not pkgdown
+ kbl
+
+ # return_type="data.frame" is a data.frame with HTML contents
+ kdf3 <- kable_coloring(
+ return_type="data.frame",
+ df=expt_df,
+ colorSub=colorSub)
+ kdf3;
+ ## Don't show:
+ }) # examplesIf
> expt_df <- data.frame(Sample_ID = "", Treatment = rep(c("Vehicle", "Dex"),
+ each = 6), Genotype = rep(c("Wildtype", "Knockout"), each = 3), Rep = paste0("rep",
+ c(1:3)))
> expt_df$Sample_ID <- pasteByRow(expt_df[, 2:4])
> colorSub <- c(Vehicle = "palegoldenrod", Dex = "navy", Wildtype = "gold",
+ Knockout = "firebrick", nameVector(color2gradient("grey48", n = 3, dex = 10),
+ rep("rep", 3), suffix = ""), nameVector(color2gradient(n = 3, c("goldenrod1",
+ "indianred3", "royalblue3", "darkorchid4")), expt_df$Sample_ID))
> kbl <- kable_coloring(expt_df, caption = "Experiment design table showing categorical color assignment.",
+ colorSub)
Error in kable_coloring(expt_df, caption = "Experiment design table showing categorical color assignment.", :
kable_coloring() requires the kableExtra package.
Calls: <Anonymous> ... source -> withVisible -> eval -> eval -> kable_coloring
Execution halted
Ran 3/3 deferred expressions
Flavor: r-oldrel-macos-arm64
Version: 1.0.2
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘jamba-vignette.Rmd’ using rmarkdown
Quitting from lines 547-570 [kable_coloring] (jamba-vignette.Rmd)
Error: processing vignette 'jamba-vignette.Rmd' failed with diagnostics:
kable_coloring() requires the kableExtra package.
--- failed re-building ‘jamba-vignette.Rmd’
SUMMARY: processing the following file failed:
‘jamba-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64